This question is specific to pdf2djvu. pdf2djvu and other pdf/djvu FOSS tools are available for both windows and Ubuntu, so I am posting a working solution here.
At the time of writing, I am using pdf2djvu on a Windows machine.

After downloading and splitting your PDF into hundreds of single-page PDFs (using pdftk), I ran pdf2djvu over all files. It turns out that only the Cover page has some problem with pdf2djvu, rest of the PDFs are easily converted to DJVU.
In DOS it was a single line: